In all honesty Magneto really isn't a villain...more like Anti-hero. Same for Catwoman. Joker by far is #1. Based off this I assume this more of a popularity contest. Going by popularity this list make perfect sense.

ok they completely ruined this where the hell is trigon supermanprime eclipso harvest black manta atrocitus prometheus the crime syndicate time trapper nekron imperiex the hood vulcan morbius ultron chemo black mask guardians of the universe and lex luthor even here and some of these guys are neutral